The 289 4V intake will do perfectly. Best to go with the C4OE-9425-B casting as it was used on the 64 Comets and early 64½ Mustangs. You can also used the C5OE-9425-A dated in May and June 64. This will be a direct swap for your 260 intake. Others will work as well, but could have different temperature senders, thermostat housings, or machining. The perfect 4V carb is 1.08 C4GF (stay away from the 1.12 C4GF's) and any C5ZF 4V. These were the best 4Vs ever produced. The 4V carb sits 1/4" more forward than the 2V, but you can easily adjust for that. This setup works equally well on the 221. There is a mismatch in intake runners with the 260/221 heads (4V intake larger), but will cause no problems. The 4V will wake up the 260 and make the engine pull harder in all rpm ranges. Fuel economy only affected to the degree of your lead foot.
For those who don't know, there is a new PDF version of "Mustang & Ford Small Block V8, 1962-1969" available at www.fordsmallblock.com
. You can read all about it there.